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- PDB-2nq8: Malarial enoyl acyl ACP reductase bound with INH-NAD adduct -

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Basic information

Entry
Database: PDB / ID: 2nq8
TitleMalarial enoyl acyl ACP reductase bound with INH-NAD adduct
Components(Enoyl-acyl carrier reductase) x 2
KeywordsOXIDOREDUCTASE / PfENR / INH / malaria
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function
Enoyl acyl carrier protein reductase / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Helicase, Ruva Protein; domain 3 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-ZID / Enoyl-ACP reductase / Enoyl-ACP reductase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFreundlich, J.S. / Yu, M. / Lucumi, E. / Kuo, M. / Tsai, H.C. / Valderramos, J.C. / Karagyozov, L. / Jacobs Jr., W.R. / Schiehser, G.A. / Fidock, D.A. ...Freundlich, J.S. / Yu, M. / Lucumi, E. / Kuo, M. / Tsai, H.C. / Valderramos, J.C. / Karagyozov, L. / Jacobs Jr., W.R. / Schiehser, G.A. / Fidock, D.A. / Jacobus, D.P. / Sacchettini, J.C.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: X-ray structural analysis of Plasmodium falciparum enoyl acyl carrier protein reductase as a pathway toward the optimization of triclosan antimalarial efficacy
Authors: Freundlich, J.S. / Wang, F. / Tsai, H.C. / Kuo, M. / Shieh, H.M. / Anderson, J.W. / Nkrumah, L.J. / Valderramos, J.C. / Yu, M. / Kumar, T.R. / Valderramos, S.G. / Jacobs, W.R. / Schiehser, G. ...Authors: Freundlich, J.S. / Wang, F. / Tsai, H.C. / Kuo, M. / Shieh, H.M. / Anderson, J.W. / Nkrumah, L.J. / Valderramos, J.C. / Yu, M. / Kumar, T.R. / Valderramos, S.G. / Jacobs, W.R. / Schiehser, G.A. / Jacobus, D.P. / Fidock, D.A. / Sacchettini, J.C.
History
DepositionOct 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-acyl carrier reductase
B: Enoyl-acyl carrier reductase
C: Enoyl-acyl carrier reductase
D: Enoyl-acyl carrier reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6866
Polymers65,1484
Non-polymers1,5372
Water2,882160
1
A: Enoyl-acyl carrier reductase
B: Enoyl-acyl carrier reductase
C: Enoyl-acyl carrier reductase
D: Enoyl-acyl carrier reductase
hetero molecules

A: Enoyl-acyl carrier reductase
B: Enoyl-acyl carrier reductase
C: Enoyl-acyl carrier reductase
D: Enoyl-acyl carrier reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,37112
Polymers130,2978
Non-polymers3,0744
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area35510 Å2
ΔGint-222 kcal/mol
Surface area39130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.899, 131.899, 82.845
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a teramer generated from the dimer in the asymmetric unit

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Components

#1: Protein Enoyl-acyl carrier reductase / Enoyl-ACP reductase


Mass: 25744.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: FabI / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BH77, UniProt: Q9BJJ9*PLUS
#2: Protein Enoyl-acyl carrier reductase / Enoyl-ACP reductase


Mass: 6829.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: FabI / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BH77
#3: Chemical ChemComp-ZID / ISONICOTINIC-ACETYL-NICOTINAMIDE-ADENINE DINUCLEOTIDE


Mass: 768.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H30N8O15P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.4M (NH4)2SO4, 0.1M MES ( PH 5.6), VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 121 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 2000 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→70.15 Å / Num. all: 25925 / Num. obs: 24589 / % possible obs: 94.8 % / Observed criterion σ(I): 1
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 15.18 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 0.71 / Num. unique all: 3280 / Rsym value: 0.277 / % possible all: 99.76

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
CNSrefinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NHD

1nhd
PDB Unreleased entry


Resolution: 2.5→70.15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 2379 -RANDOM
Rwork0.216 ---
all0.2161 25859 --
obs0.2161 24177 93.5 %-
Displacement parametersBiso mean: 39.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å20 Å20 Å2
2--2.59 Å20 Å2
3----5.179 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.5→70.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4578 0 104 160 4842
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_bond_d0.007

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